BasicStructureIO.hh

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#ifndef CASM_xtal_BasicStructure_io
#define CASM_xtal_BasicStructure_io
 
#include <boost/filesystem/path.hpp>
#include <map>
#include <string>
 
#include "casm/global/definitions.hh"
#include "casm/global/eigen.hh"
#include "casm/global/enum.hh"
 
namespace CASM {
namespace xtal {
class Lattice;
class SpeciesAttribute;
class AtomPosition;
class Molecule;
class Site;
class BasicStructure;
}  // namespace xtal
 
// --- These functions are for casm I/O -----------
 
class AnisoValTraits;
template <typename T>
class ParsingDictionary;
template <typename T>
struct jsonConstructor;
class jsonParser;
 
// --------- PrimIO Declarations
// --------------------------------------------------
 
jsonParser const &from_json(xtal::SpeciesAttribute &_attr,
                            jsonParser const &json);
 
jsonParser &to_json(xtal::SpeciesAttribute const &_attr, jsonParser &json);
 
jsonParser &to_json(const xtal::AtomPosition &apos, jsonParser &json,
                    Eigen::Ref<const Eigen::Matrix3d> const &cart2frac);
 
void from_json(xtal::AtomPosition &apos, const jsonParser &json,
               Eigen::Ref<const Eigen::Matrix3d> const &frac2cart,
               ParsingDictionary<AnisoValTraits> const &_aniso_val_dict);
 
template <>
struct jsonConstructor<xtal::AtomPosition> {
  static xtal::AtomPosition from_json(
      const jsonParser &json, Eigen::Matrix3d const &f2c_mat,
      ParsingDictionary<AnisoValTraits> const &_aniso_val_dict);
};
 
jsonParser &to_json(const xtal::Molecule &mol, jsonParser &json,
                    Eigen::Ref<const Eigen::Matrix3d> const &c2f_mat);
 
void from_json(xtal::Molecule &mol, const jsonParser &json,
               Eigen::Ref<const Eigen::Matrix3d> const &f2c_mat,
               ParsingDictionary<AnisoValTraits> const &_aniso_val_dict);
 
template <>
struct jsonConstructor<xtal::Molecule> {
  static xtal::Molecule from_json(
      const jsonParser &json, Eigen::Ref<const Eigen::Matrix3d> const &f2c_mat,
      ParsingDictionary<AnisoValTraits> const &_aniso_val_dict);
};
 
template <>
struct jsonConstructor<xtal::Site> {
  static xtal::Site from_json(
      const jsonParser &json, xtal::Lattice const &_home, COORD_TYPE coordtype,
      std::map<std::string, xtal::Molecule> const &mol_map,
      ParsingDictionary<AnisoValTraits> const &_aniso_val_dict);
};
 
jsonParser &to_json(const xtal::Site &value, jsonParser &json,
                    COORD_TYPE coordtype);
 
void from_json(xtal::Site &value, const jsonParser &json,
               xtal::Lattice const &_home, COORD_TYPE coordtype,
               std::map<std::string, xtal::Molecule> const &mol_map,
               ParsingDictionary<AnisoValTraits> const &_aniso_val_dict);
 
xtal::BasicStructure read_prim(
    fs::path filename, double xtal_tol,
    ParsingDictionary<AnisoValTraits> const *_aniso_val_dict = nullptr);
 
xtal::BasicStructure read_prim(
    jsonParser const &json, double xtal_tol,
    ParsingDictionary<AnisoValTraits> const *_aniso_val_dict = nullptr);
 
void write_prim(const xtal::BasicStructure &prim, fs::path filename,
                COORD_TYPE mode, bool include_va = false);
 
void write_prim(const xtal::BasicStructure &prim, jsonParser &json,
                COORD_TYPE mode, bool include_va = false);
 
void from_json(
    xtal::BasicStructure &prim, jsonParser const &json, double xtal_tol,
    ParsingDictionary<AnisoValTraits> const *_aniso_val_dict = nullptr);
 
jsonParser &to_json(const xtal::BasicStructure &prim, jsonParser &json,
                    COORD_TYPE mode, bool include_va = false);
 
}  // namespace CASM
 
#endif